Molecular Ecology Resources最新文献

{"title":"Temporal Variability in Effective Size (\u0000 \u0000 \u0000 \u0000 \u0000 N\u0000 ̂\u0000 \u0000 e\u0000 \u0000 \u0000 ) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance","authors":"Daniel E. Ruzzante, Gregory R. McCracken, Dylan J. Fraser, John MacMillan, Colin Buhariwalla, Joanna Mills Flemming","doi":"10.1111/1755-0998.14047","DOIUrl":"10.1111/1755-0998.14047","url":null,"abstract":"<p>Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Here we took advantage of a rich dataset of seven brook trout (<i>Salvelinus fontinalis</i>) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 </mrow>\u0000 </semantics></math><sub><i>b</i></sub>) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>b</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> and subsequently, <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>e</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> following Waples et al. (2013). <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>e</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 ","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant","authors":"Shao Shao,&nbsp;Yulong Li,&nbsp;Xiao Feng,&nbsp;Chuanfeng Jin,&nbsp;Min Liu,&nbsp;Ranran Zhu,&nbsp;Miles E. Tracy,&nbsp;Zixiao Guo,&nbsp;Ziwen He,&nbsp;Suhua Shi,&nbsp;Shaohua Xu","doi":"10.1111/1755-0998.14045","DOIUrl":"10.1111/1755-0998.14045","url":null,"abstract":"<div>\u0000 \u0000 <p>Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree <i>Pellacalyx yunnanensis</i>, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that <i>P. yunnanensis</i> has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that <i>P. yunnanensis</i> is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of <i>P. yunnanensis</i> to future climate change, informing future conservation efforts.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of SNP Panels from Low-Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada","authors":"Anne Beemelmanns,&nbsp;Raphaël Bouchard,&nbsp;Sozos Michaelides,&nbsp;Eric Normandeau,&nbsp;Hyung-Bae Jeon,&nbsp;Badrouyk Chamlian,&nbsp;Charles Babin,&nbsp;Philippe Hénault,&nbsp;Océane Perrot,&nbsp;Les N. Harris,&nbsp;Xinhua Zhu,&nbsp;Dylan Fraser,&nbsp;Louis Bernatchez †,&nbsp;Jean-Sébastien Moore","doi":"10.1111/1755-0998.14040","DOIUrl":"10.1111/1755-0998.14040","url":null,"abstract":"<p>Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (<i>Salvelinus alpinus</i>), Brook Trout (<i>Salvelinus fontinali</i>s) and Lake Whitefish (<i>Coregonus clupeaformis</i>) are among the most harvested and consumed fish species in Northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in Northern Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec) and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated using 525 individuals with an average assignment accuracy of 83%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed-stock fisheries across multiple regions. Interweaving genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14040","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations","authors":"Satoshi Hiraoka,&nbsp;Minoru Ijichi,&nbsp;Hirohiko Takeshima,&nbsp;Yohei Kumagai,&nbsp;Ching-Chia Yang,&nbsp;Yoko Makabe-Kobayashi,&nbsp;Hideki Fukuda,&nbsp;Susumu Yoshizawa,&nbsp;Wataru Iwasaki,&nbsp;Kazuhiro Kogure,&nbsp;Takuhei Shiozaki","doi":"10.1111/1755-0998.14042","DOIUrl":"10.1111/1755-0998.14042","url":null,"abstract":"<p>The ammonia monooxygenase subunit A (<i>amoA</i>) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of <i>amoA</i> is a widely used method; however, it produces inaccurate results owing to the lack of a ‘universal’ primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for <i>amoA</i> enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched <i>amoA</i> genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or <i>amoA</i> gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors","authors":"Jiaying Li,&nbsp;Yuze Gao,&nbsp;Guocheng Shu,&nbsp;Xuanzhong Chen,&nbsp;Jiahao Zhu,&nbsp;Si Zheng,&nbsp;Ting Chen","doi":"10.1111/1755-0998.14046","DOIUrl":"10.1111/1755-0998.14046","url":null,"abstract":"<div>\u0000 \u0000 <p>Symbiotic microbiota strongly impact host physiology. Amphibians and reptiles occupy a pivotal role in the evolutionary history of Animalia, and they are of significant ecological, economic, and scientific value. Many prior studies have found that symbiotic microbiota in herpetofaunal species are closely associated with host phylogeny, physiological traits, and environmental factors; however, insufficient integrated databases hinder researchers from querying, accessing, and reanalyzing these resources. To rectify this, we built the first herpetofaunal microbiota database (HMicroDB; https://herpdb.com/) that integrates 11,697 microbiological samples from 337 host species (covering 23 body sites and associated with 23 host phenotypic or environmental factors), and we identified 11,084 microbial taxa by consistent annotation. The standardised analysis process, cross-dataset integration, user-friendly interface, and interactive visualisation make the HMicroDB a powerful resource for researchers to search, browse, and explore the relationships between symbiotic microbiota, hosts, and environment. This facilitates research in host–microbiota coevolution, biological conservation, and resource utilisation.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OGU: A Toolbox for Better Utilising Organelle Genomic Data","authors":"Ping Wu,&nbsp;Ningning Xue,&nbsp;Jie Yang,&nbsp;Qiang Zhang,&nbsp;Yuzhe Sun,&nbsp;Wen Zhang","doi":"10.1111/1755-0998.14044","DOIUrl":"10.1111/1755-0998.14044","url":null,"abstract":"<p>Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14044","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to “Characterisation of Putative Circular Plasmids in Sponge-Associated Bacterial Communities Using a Selective Multiply-Primed Rolling Circle Amplification”","authors":"","doi":"10.1111/1755-0998.14043","DOIUrl":"10.1111/1755-0998.14043","url":null,"abstract":"<p>Oliveira, V., A. R. M. Polónia, D. F. R. Cleary, et al. 2021. “Characterization of putative circular plasmids in sponge-associated bacterial communities using a selective multiply-primed rolling circle amplification.” <i>Molecular Ecology Resources</i> <b>21</b>, no. 1: 110–121. https://doi.org/10.1111/1755-0998.13248.</p><p>The authors of the above article noticed an error in the DNA concentration which is detailed in the ‘Methods’ section, section 2.3 (‘Selective multiply-primed rolling circle amplification’), paragraph 2. The correct text should read as ‘1 μL template DNA (ca. 200 ng)’.</p><p>The authors apologise for this error and any inconvenience it may have caused.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Chromosome-Scale Genome of Magnolia sieboldii K. Koch Provides Insight Into the Evolutionary Position of Magnoliids and Seed Germination","authors":"Xiujun Lu,&nbsp;Mei Mei,&nbsp;Lin Liu,&nbsp;Xin Xu,&nbsp;Wanfeng Ai","doi":"10.1111/1755-0998.14030","DOIUrl":"10.1111/1755-0998.14030","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Magnolia sieboldii</i> K. Koch (<i>M. sieboldii</i>) stands as an elegant tree species within the Magnoliaceae family, esteemed for its exquisite beauty, cultural significance and economic advantages. The species faces challenges in seed germination under natural conditions, primarily attributed to morphological dormancy. Despite its significance, the molecular mechanisms governing <i>M. sieboldii</i> seed germination remain elusive, compounded by the absence of genomic resources specific to this species. In this study, we present the first chromosome-scale genome assembly of <i>M. sieboldii</i>, with a total genome size of 2.01 Gb, including 1096 scaffolds assigned to 19 chromosomes (N50 = 102.4 Mb). Phylogenetic analyses, incorporating 13 plant species, illuminate the evolutionary independence of Magnoliids from monocots and eudicots, positioning them as a sister clade. Through RNA-seq analysis, we identify pivotal genes and pathways contributing to seed dormancy and germination. In addition, our investigation delves into the the far-red-impaired response (FAR1) transcription factor gene family, revealing their enrichment throughout evolution and their involvement in the intricate process of seed germination. This comprehensive genome sequencing initiative offers invaluable insights into the biological attributes of <i>M. sieboldii</i>, with a specific emphasis on unravelling the complexities of seed dormancy and germination.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections","authors":"Oliver W. White,&nbsp;Andie Hall,&nbsp;Ben W. Price,&nbsp;Suzanne T. Williams,&nbsp;Matthew D. Clark","doi":"10.1111/1755-0998.14036","DOIUrl":"10.1111/1755-0998.14036","url":null,"abstract":"<p>Low coverage ‘genome-skims’ are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines <i>skim2mito</i>, <i>skim2rrna</i> and <i>gene2phylo</i>, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, <i>skim2mito</i> and <i>skim2rrna</i> perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline <i>gene2phylo</i> takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance","authors":"Ben J. Wiens,&nbsp;Jocelyn P. Colella","doi":"10.1111/1755-0998.14039","DOIUrl":"10.1111/1755-0998.14039","url":null,"abstract":"<div>\u0000 \u0000 <p>Describing naturally occurring genetic variation is a fundamental goal of molecular phylogeography and population genetics. Popular methods for this task include <i>STRUCTURE</i>, a model-based algorithm that assigns individuals to genetic clusters, and principal component analysis (PCA), a parameter-free method. The ability of <i>STRUCTURE</i> to infer mixed ancestry makes it popular for documenting natural hybridisation, which is of considerable interest to evolutionary biologists, given that such systems provide a window into the speciation process. Yet, <i>STRUCTURE</i> can produce misleading results when its underlying assumptions are violated, like when genetic variation is distributed continuously across geographic space. To test the ability of <i>STRUCTURE</i> and PCA to accurately distinguish admixture from continuous variation, we use forward-time simulations to generate population genetic data under three demographic scenarios: two involving admixture and one with isolation by distance (IBD). <i>STRUCTURE</i> and PCA alone cannot distinguish admixture from IBD, but complementing these analyses with triangle plots, which visualise hybrid index against interclass heterozygosity, provides more accurate inference of demographic history, especially in cases of recent admixture. We demonstrate that triangle plots are robust to missing data, while <i>STRUCTURE</i> and PCA are not, and show that setting a low allele frequency difference threshold for ancestry-informative marker (AIM) identification can accurately characterise the relationship between hybrid index and interclass heterozygosity across demographic histories of admixture and range expansion. While <i>STRUCTURE</i> and PCA provide useful summaries of genetic variation, results should be paired with triangle plots before admixture is inferred.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}